A resource dependent protein synthesis model for evaluating synthetic circuits

TL;DR

This paper introduces a novel resource-dependent protein synthesis model based on the Ribosome Flow Model, enabling better in-silico evaluation of synthetic gene circuits by capturing resource limitations and dynamic behaviors.

Contribution

The paper presents a new protein synthesis model that incorporates resource limitations and analyzes its convergence, providing a tool for evaluating synthetic gene circuit performance.

Findings

Model describes RNA-polymerase and ribosome movement on templates.

Convergence analysis offers insights into synthesis dynamics.

Application demonstrates evaluation of synthetic circuits under various loads.

Abstract

Reliable in-silico design of synthetic gene networks necessitates novel approaches to model the process of protein synthesis under the influence of limited resources. We present such a novel protein synthesis model which originates from the Ribosome Flow Model and among other things describes the movement of RNA-polymerase and Ribosomes on mRNA and DNA templates respectively. By analyzing the convergence properties of this model based upon geometric considerations we present additional insights into the dynamic mechanisms of the process of protein synthesis. Further, we exemplarily show how this model can be used to evaluate the performance of synthetic gene circuits under different loading scenarios.